The time resolved transcriptome of C. elegans
- Max E Boeck1,
- Chau Huynh2,
- Lou Gevirtzman3,
- Owen A Thompson3,
- Guilin Wang4,
- Dionna M Kasper4,
- Valerie Reinke4,
- LaDeana W Hillier3 and
- Robert H Waterston3,5
- 1 Regis University;
- 2 Univesity of Washington;
- 3 University of Washington;
- 4 Yale School of Medicine
- ↵* Corresponding author; email: waterston{at}gs.washington.edu
Abstract
We have generated detailed RNA-seq data for the nematode C. elegans with high temporal resolution in the embryo as well as representative samples from postembryonic stages across life cycle. The data reveal that early and late embryogenesis is accompanied by large numbers of genes changing expression, whereas fewer genes are changing in mid-embryogenesis. This lull in genes changing expression correlates with a period where histone mRNAs produce almost 40% of the RNA-seq reads. We find evidence for many more splice junctions than are annotated in WormBase, with many of these suggesting alternative splice forms, often with differential usage over the life cycle. We have annotated internal promoter usage in operons using SL1 and SL2 data. We have also uncovered correlated transcriptional programs that span more than 80kb. These data provide detailed annotation of the C. elegans transcriptome.
- Received December 2, 2015.
- Accepted August 15, 2016.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International license), as described at http://creativecommons.org/licenses/by/4.0/.
